Variant report

Variant	rs518216
Chromosome Location	chr1:46037357-46037358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45266030..45268033-chr1:46037084..46039498,2	K562	blood:
2	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
3	chr1:45986033..45988410-chr1:46036491..46038033,2	MCF-7	breast:
4	chr1:46030852..46033129-chr1:46036689..46038805,2	K562	blood:
5	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
6	chr1:46035896..46038206-chr1:46048014..46050744,2	MCF-7	breast:
7	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
8	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
9	chr1:46034190..46037574-chr1:46047982..46052662,9	K562	blood:
10	chr1:45804838..45807307-chr1:46034691..46038164,3	K562	blood:
11	chr1:46035115..46037673-chr1:46042096..46043959,2	K562	blood:
12	chr1:45973201..45975772-chr1:46035832..46037703,2	K562	blood:
13	chr1:46029652..46033129-chr1:46033927..46038189,5	K562	blood:
14	chr1:46035047..46037595-chr1:46039672..46041229,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132763	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10430105	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs10430123	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap]
rs10430124	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs10749856	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10789467	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10789470	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap]
rs10789471	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[MKK][hapmap]
rs1084086	0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[MKK][hapmap]
rs10890333	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs10890334	0.86[CHB][hapmap]
rs10890335	0.86[CHB][hapmap]
rs10890336	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10890341	0.86[CHB][hapmap]
rs10890346	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.82[MKK][hapmap]
rs11211124	0.81[GIH][hapmap]
rs11211129	0.82[CHD][hapmap]
rs11211142	1.00[ASN][1000 genomes]
rs11211145	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[MKK][hapmap]
rs11211147	0.89[CHB][hapmap]
rs11211149	0.90[CHB][hapmap]
rs11211152	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs11211157	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs11211160	0.86[CHB][hapmap]
rs11211161	0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs11211163	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap]
rs11211166	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11211168	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[MKK][hapmap]
rs11211169	0.82[CHB][hapmap];0.95[CHD][hapmap];0.83[MKK][hapmap]
rs11211171	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs11211173	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs11211177	0.90[CHD][hapmap];0.82[MKK][hapmap]
rs11211178	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11211181	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs1135812	0.86[CHB][hapmap]
rs12023439	0.85[CHB][hapmap]
rs12024590	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs12029322	0.81[GIH][hapmap]
rs12037459	0.89[CHB][hapmap]
rs12043945	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12049027	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12049503	0.90[GIH][hapmap]
rs12091503	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1250	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs1547924	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs1547925	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[MKK][hapmap]
rs1972410	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs2050376	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs2088102	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2152078	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[MKK][hapmap]
rs2230657	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2230658	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs2230659	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2253862	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs2275085	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap]
rs2275086	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[MKK][hapmap]
rs28370457	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[MKK][hapmap]
rs28375469	0.81[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs28550303	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs28647556	0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs28719889	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs28817701	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap]
rs28890893	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs2934857	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2934858	0.97[ASN][1000 genomes]
rs2934859	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2991972	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2991973	0.82[ASN][1000 genomes]
rs2991976	0.99[ASN][1000 genomes]
rs2991977	0.88[ASN][1000 genomes]
rs2991979	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[MKK][hapmap]
rs2991981	0.88[ASN][1000 genomes]
rs2991986	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs2991987	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2991988	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs2991989	0.86[CHB][hapmap]
rs2993263	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs3013595	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs3013597	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3014210	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs3014212	0.88[ASN][1000 genomes]
rs3014216	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3014218	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3014219	0.84[ASN][1000 genomes]
rs3014235	0.86[CHB][hapmap]
rs3014237	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs3014238	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs3014239	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs3014241	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs3014242	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.86[MKK][hapmap]
rs3014245	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs3014251	0.83[ASN][1000 genomes]
rs3790585	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs3811436	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs4274104	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4391704	0.89[CHB][hapmap]
rs4431884	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4439382	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs4468203	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4559551	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap]
rs4564187	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4607935	0.90[CHB][hapmap]
rs4609469	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4633317	0.81[GIH][hapmap]
rs4660312	0.84[CHB][hapmap];0.95[CHD][hapmap]
rs4660313	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[MKK][hapmap]
rs4660863	0.81[GIH][hapmap]
rs4660880	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[MKK][hapmap]
rs4660882	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4660883	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[MKK][hapmap]
rs499600	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5021934	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs512026	0.81[JPT][hapmap]
rs514595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs518365	0.82[CHD][hapmap]
rs563799	0.95[ASN][1000 genomes]
rs622798	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs6429576	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs659437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656279	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6658700	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs6694889	0.86[CHB][hapmap]
rs6697821	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap]
rs6703748	0.86[CHB][hapmap]
rs7545118	0.80[ASN][1000 genomes]
rs7547414	0.82[ASN][1000 genomes]
rs868351	0.85[GIH][hapmap]
rs9429172	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs518216	IPP	cis	lymphoblastoid	seeQTL
rs518216	CYP4Z2P	cis	cerebellum	SCAN
rs518216	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs518216	ST3GAL3	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:46018600-46037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:46018600-46038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:46025800-46037800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:46026800-46038600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:46028200-46037400	Strong transcription	Fetal Intestine Large	intestine
9	chr1:46028200-46038800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:46031400-46037400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:46031400-46037400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:46031600-46037400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:46032000-46037400	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr1:46032400-46037400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:46032400-46037400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:46032600-46037400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:46032600-46049000	Weak transcription	Right Atrium	heart
18	chr1:46033000-46048800	Weak transcription	Fetal Brain Male	brain
19	chr1:46034000-46037400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:46034200-46039800	Weak transcription	Small Intestine	intestine
21	chr1:46034200-46048800	Weak transcription	Stomach Mucosa	stomach
22	chr1:46035000-46041000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:46035000-46042600	Weak transcription	HMEC	breast
24	chr1:46035200-46039600	Weak transcription	Fetal Heart	heart
25	chr1:46035400-46039200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:46035400-46039600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:46035400-46048800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:46035600-46048000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:46035600-46048800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:46035800-46038600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:46035800-46039600	Weak transcription	Aorta	Aorta
32	chr1:46035800-46039600	Weak transcription	Colonic Mucosa	Colon
33	chr1:46035800-46039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:46035800-46040000	Weak transcription	Left Ventricle	heart
35	chr1:46035800-46041000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:46035800-46041800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:46035800-46048800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:46035800-46048800	Weak transcription	Hela-S3	cervix
39	chr1:46036000-46039600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:46036200-46038800	Weak transcription	Esophagus	oesophagus
41	chr1:46036200-46039000	Weak transcription	Pancreas	Pancrea
42	chr1:46036200-46047600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:46036200-46048800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:46036400-46038800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:46036400-46039000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:46036400-46039200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:46036400-46039200	Weak transcription	Ovary	ovary
48	chr1:46036400-46039400	Weak transcription	Right Ventricle	heart
49	chr1:46036400-46039600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:46036400-46039800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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